X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedsobscollectsummary.cpp;h=b53b09afc0091e91baf6609aa9c8d5b0ab528b63;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=0096303d03cd8282e8732046ddc36205a15a1633;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/sharedsobscollectsummary.cpp b/sharedsobscollectsummary.cpp
index 0096303..b53b09a 100644
--- a/sharedsobscollectsummary.cpp
+++ b/sharedsobscollectsummary.cpp
@@ -16,10 +16,10 @@
 EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared){
 	try {
 		data.resize(1,0);
-		int observed = 0;
+		double observed = 0;
 		int numGroups = shared.size();
 
-		for (int i = 0; i < shared[0]->size(); i++) {
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
 			//get bin values and set sharedByAll 
 			bool sharedByAll = true;
 			for (int j = 0; j < numGroups; j++) {
@@ -34,7 +34,37 @@ EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared){
 		return data;
 	}
 	catch(exception& e) {
-		errorOut(e, "SharedSobsCS", "getValues");
+		m->errorOut(e, "SharedSobsCS", "getValues");
+		exit(1);
+	}
+}
+/***********************************************************************/
+//This returns the number of shared species observed in several groups.  
+//The shared vector is each groups sharedrabundvector.
+
+EstOutput SharedSobsCS::getValues(vector<SharedRAbundVector*> shared, vector<string>& labels){
+	try {
+		data.resize(1,0);
+		double observed = 0;
+		int numGroups = shared.size();
+        labels.clear();
+        
+		for (int i = 0; i < shared[0]->getNumBins(); i++) {
+			//get bin values and set sharedByAll 
+			bool sharedByAll = true;
+			for (int j = 0; j < numGroups; j++) {
+				if (shared[j]->getAbundance(i) == 0) { sharedByAll = false; }
+			}
+			
+			//they are shared
+			if (sharedByAll == true) {  observed++;  labels.push_back(m->currentBinLabels[i]); }
+		}
+        
+		data[0] = observed;
+		return data;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SharedSobsCS", "getValues");
 		exit(1);
 	}
 }